fix hist limit issue for step* for both linear and log scale #1075

piti118 · 2012-08-12T11:56:15Z

Fix two closely related issue:
#1066

WeatherGod · 2012-08-14T02:20:51Z

lib/matplotlib/axes.py

@@ -7946,6 +7946,22 @@ def hist(self, x, bins=10, range=None, normed=False, weights=None,
                x += 0.5*(bins[1]-bins[0])

            if log:
+                #in the case of log scale there are three cases to consider for the y axis limit
+                #1) has zero or negative bin but other bins may be 0<n<1 due to weighting. we want positive minimum*0.1 to be the minimum


Please keep within 80 characters line width as per PEP8.

mdboom · 2012-08-14T05:16:31Z

lib/matplotlib/axes.py

+
+                if np.any(ndata>0):
+                    if np.all(ndata[ndata!=0]>=1):
+                        minimum = 0.1 # case 2)


Shouldn't this be log_base ** -1? (i.e. 0.1 only makes sense when the log base is 10).

Yes, but how do I access the base of log scale axis?

Ah, I see. I missed the fact that hist doesn't take a base as argument. hist is a bit of an anomaly -- it takes a 'log' argument, whereas most other things (except bar*) work by requiring a subsequent call to set_xscale or set_yscale, which of course take an optional "base". Making this also work that way would be a little bit of work, because this minimum adjustment stuff you've added here would have to be moved to the draw phase. Ideally, that's where I'd like to see this go, but I don't know if that's worth abandoning this fix, and we've have to maintain backward compatiblity anyway -- this "log" kwarg goes back at least 5 years, as far as I can tell.

We could either add an additional keyword "log_base", or extend "log" so it can be "True" (meaning base 10 as it does now), or a number, meaning a base. I would also recommend updating bar* to be in line with that.

However, I'm aware that none of this is premised on any real world use case -- just my own desire for consistency across uses of log scale, so I could be persuaded to leave this as-is by further discussion.

This might be kind of hard to set the minimum correctly if log base can be changed between to calls. Consider this

ax.hist( x1, log=10) ax.hist(x2, log=2)

The first hist call would have no idea that eventually the base of log scale will be changed to 2.

But, I do not think it would be hard for use to do another call to set_ylim though. The histogram will be painted all the way down (see line 7892) anyway.

Yes -- that, in a nutshell, is why I'm not a fan of "log" being a kwarg to this method. You may want to hold of on implementing any sort of fix for this issue until we discuss it -- it may be best to just leave as-is.

@efiring, @WeatherGod, @pelson: any thoughts?

w.r.t. not being able to access the axes's log base, we are assuming base 10 throughout this part of the code, and we have always done so before. We could always look to future PRs to address the handling of arbitrary log bases. I see this more as a good bug fix to an outstanding issue.

I guess it would be smart, though, for future developers, to somehow comment the spots that are assuming base 10 so that they know to change it if/when we extend the interface in the future to accept arbitary log bases.

I tend to agree with @WeatherGod here: let's leave this assuming base 10 for now.

WeatherGod · 2012-08-14T20:41:17Z

log in hist has always been an odd duck. It tries to be like the bar* functions, but not quite. Note, however, that unlike the bar* functions, a log kwarg in hist actually has a purpose besides convenience. While one could pre-transform their data for the bar* functions, one can't with hist because what is plotted is the result of an internal aggregation calculation.

There is another PR that I am waiting for a few last polishings that also addresses an issue for log scaling of the results for hist2d(). Might be a good idea to make sure both functions support the same "log" kwarg inputs.

WeatherGod · 2012-08-17T02:41:33Z

lib/matplotlib/axes.py

@@ -7946,7 +7946,29 @@ def hist(self, x, bins=10, range=None, normed=False, weights=None,
                x += 0.5*(bins[1]-bins[0])

            if log:
-                y[0],y[-1] = minimum, minimum
+                #in the case of log scale there are three cases 


Wrap these comment lines to less than 75 characters

75? I thought we did 80?

Actually, I was wrong, in PEP8, docstrings are recommended to be at most 72 characters.

WeatherGod · 2012-08-17T02:55:45Z

Great job with the additional tests. Only one request here about them. Think we could have corresponding tests for the horizontal case?

WeatherGod · 2012-08-17T04:40:10Z

lib/matplotlib/axes.py

@@ -7970,22 +7996,14 @@ def hist(self, x, bins=10, range=None, normed=False, weights=None,

            # adopted from adjust_x/ylim part of the bar method
            if orientation == 'horizontal':
-                xmin0 = max(_saved_bounds[0]*0.9, minimum)
+                xmin = minimum


My comments above wrt multiple calls to hist() goes here.

This is kind of the part I don't fully understand. What function does 0.9 serve and where should I get the old bound. What's the difference between self.datalim.bound and self.datalim.intervalx/y?

I don't have time for a full explanation as I am about to head off on
vacation, but perhaps I can provide some clues for you. I think this code
part has been neglected. Other functions like plot() and scatter() utilize
pads for the data limits so that the axes wouldn't be extremely tight
around the data being plotted. This value used to be a hard-coded 0.05 on
each endside (for a total of 0.1). In plot() and scatter() (and possibly
bar()) we now handle this a lot more intelligently, but I think hist() was
left behind in this regard.

Note that data limits don't necessarially mean the same as view limits. I
am not sure what the distinction is between data limits and data interval
is, though.

I hope this helps!
Ben Root

lpsinger · 2013-01-01T01:45:01Z

Does this pull request need any more work? histtype='stepfilled' also produces pretty unsightly results on master.

piti118 · 2013-01-01T04:09:02Z

I think it needs testing on multiple plots being drawn together. I'm not 100% sure what _save_bounds does.

dmcdougall · 2013-01-27T18:13:09Z

I just saw this. #1684 was merged and #196 was closed. Does this PR also need to be merged? I.e., does it fix a separate issue not addressed in #1684?

piti118 · 2013-01-27T19:05:01Z

They seems to fix the same thing. I'll close this.

dmcdougall · 2013-01-27T19:19:12Z

@piti118 Judging by the title of this PR, this patch seems to address behaviour that can be seen when using a linear scale rather than a log scale. PR #1684 only addresses an issue with log scaling. Therefore it might be the case that this may need to be reopened.

Thanks for taking the time and the effort to write a patch for the codebase, @piti118.

Again, if you see unexpected behaviour with linear scaling then please feel free to re-open this.

fix hist limit issue for step* for both linear and log scale

9d6d82a

piti118 mentioned this pull request Aug 12, 2012

fix limit calculation of step* histogram #1066

Closed

fix case matplotlib#2)

0871b4a

WeatherGod reviewed Aug 14, 2012
View reviewed changes

piti118 added 2 commits August 13, 2012 21:25

Filled the histogram all the way down, PEP8 and better warning

c9b0e58

update hist_step test to reflect new changes

1beb704

mdboom reviewed Aug 14, 2012
View reviewed changes

WeatherGod reviewed Aug 17, 2012
View reviewed changes

update axes comment

48fbd80

ghost assigned dmcdougall Jan 27, 2013

piti118 closed this Jan 27, 2013

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fix hist limit issue for step* for both linear and log scale #1075

fix hist limit issue for step* for both linear and log scale #1075

piti118 commented Aug 12, 2012

WeatherGod Aug 14, 2012

mdboom Aug 14, 2012

piti118 Aug 14, 2012

mdboom Aug 14, 2012

piti118 Aug 14, 2012

mdboom Aug 14, 2012

WeatherGod Aug 17, 2012

mdboom Aug 20, 2012

WeatherGod commented Aug 14, 2012

WeatherGod Aug 17, 2012

pelson Aug 19, 2012

WeatherGod Aug 20, 2012

WeatherGod commented Aug 17, 2012

WeatherGod Aug 17, 2012

piti118 Aug 17, 2012

WeatherGod Aug 17, 2012

lpsinger commented Jan 1, 2013

piti118 commented Jan 1, 2013

dmcdougall commented Jan 27, 2013

piti118 commented Jan 27, 2013

dmcdougall commented Jan 27, 2013

fix hist limit issue for step* for both linear and log scale #1075

fix hist limit issue for step* for both linear and log scale #1075

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piti118 commented Aug 12, 2012

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WeatherGod commented Aug 14, 2012

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WeatherGod commented Aug 17, 2012

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lpsinger commented Jan 1, 2013

piti118 commented Jan 1, 2013

dmcdougall commented Jan 27, 2013

piti118 commented Jan 27, 2013

dmcdougall commented Jan 27, 2013